Browsing NTNU Open by Author "Zhang, Guojie"
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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family
Liu, Shanlin; Westbury, Michael V; Dussex, Nicolas; Mitchell, Kieren J.; Sinding, Mikkel-Holger S.; Heintzman, Peter D.; Duchêne, David A.; Kapp, Joshua D.; von Seth, Johanna; Heiniger, Holly; Sánchez-Barreiro, Fatima; Margaryan, Ashot; André-Olsen, Remi; De Cahsan, Binia; Meng, Guanliang; Yang, Chentao; Chen, Lei; van der Valk, Tom; Moodley, Yoshan; Rookmaaker, Kees; Bruford, Michael W.; Ryder, Oliver; Steiner, Cynthia; Bruins-van Sonsbeek, Linda G. R.; Vartanyan, Sergey; Guo, Chunxue; Cooper, Alan; Kosintsev, Pavel; Kirillova, Irina V.; Lister, Adrian M.; Marques-Bonet, Tomas; Gopalakrishnan, Shyam; Dunn, Robert R.; Lorenzen, Eline D.; Shapiro, Beth; Zhang, Guojie; Antoine, Pierre-Olivier; Dalén, Love; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2021)Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct ... -
Changes in the functional diversity of modern bird species over the last million years
Germain, Ryan R.; Feng, Shaohong; Buffan, Lucas; Carmona, Carlos P.; Chen, Guangii; Graves, Gary R.; Tobias, Joseph A.; Rahbek, Carsten; Lei, Fumin; Fjeldså, Jon; Hosner, Peter A.; Gilbert, Marcus Thomas Pius; Zhang, Guojie; Nogués-Bravo, David (Journal article; Peer reviewed, 2023)Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread ... -
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Mak, Sarah S.T.; Gopalakrishnan, Shyam; Carøe, Christian; Geng, Chunyu; Liu, Shanlin; Sinding, Mikkel Holger Strander; Kuderna, Lukas FK; Zhang, Wenwei; Fu, Shujin; Vieira, Filipe G.; Germonpre, Mietje; Bocherens, Hervé; Fedorov, Sergey; Petersen, Bent; Sicheritz-Pontén, Thomas; Marques-Bonet, Tomas; Zhang, Guojie; Jiang, Hui; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2017)Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant ... -
Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum): a unique insight into the history of a precious endemic bird
Cavill, Emily L.; Gopalakrishnan, Shyam; Puetz, Lara C.; Ribeiro, Ângela M.; Mak, Sarah S. T.; da Fonseca, Rute R.; Pacheco, George; Dunlop, Bronwyn; Accouche, Wilna; Shah, Nirmal; Zora, Anna; Calabrese, Licia; Genner, Martin; Jones, Gareth; Guo, Chunxue; Zhang, Guojie; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the ... -
A draft genome sequence of the elusive giant squid, Architeuthis dux
Da Fonseca, Rute R.; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe; Gardner, Paul; Baril, Tobias; Hayward, Alex; Campos, Alexandre; Ribeiro, Ângela M; Barrio-Hernandez, Inigo; Hoving, Henk-Jan; Tafur-Jimenez, Ricardo; Chu, Chong; Frazão, Barbara; Petersen, Bent; Peñaloza, Fernando; Musacchia, Francesco; Alexander, Graham C; Osório, Hugo; Winkelmann, Inger; Simakov, Oleg; Rasmussen, Simon; Rahman, M. Ziaur; Pisani, Davide; Vinther, Jakob; Jarvis, Erich D.; Zhang, Guojie; Strugnell, Jan M.; Castro, L. Filipe C; Fedrigo, Olivier; Patricio, Mateus; Li, Qiye; Rocha, Sara; Antunes, Agostinho; Wu, Yufeng; Ma, Bin; Sanges, Remo; Vinar, Tomas; Blagoev, Blagoy; Sicheritz-Pontén, Thomas; Nielsen, Rasmus; Gilbert, Marcus Thomas Pius (Peer reviewed; Journal article, 2020)Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the ... -
The Earth BioGenome Project 2020: Starting the clock
Lewin, Harris A.; Richards, Stephen; Aiden, Erez Lieberman; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine B.; Baumgartner, Bridget; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark L.; Cai, Jing; Caperello, Nicolette D.; Carlson, Keith; Castilla-Rubio, Juan Carlos; Chaw, Shu-Miaw; Chen, Lei; Childers, Anna K.; Coddington, Jonathan A.; Conde, Dalia A.; Corominas, Montserrat; Crandall, Keith A.; Crawford, Andrew J.; DiPalma, Federica; Durbin, Richard; Ebenezer, ThankGod E.; Edwards, Scott V.; Fedrigo, Olivier; Flicek, Paul; Formenti, Giulio; Gibbs, Richard A.; Gilbert, Marcus Thomas Pius; Goldstein, Melissa M.; Graves, Jennifer Marshall; Greely, Henry T.; Grigoriev, Igor V.; Hackett, Kevin J.; Hall, Neil; Haussler, David; Helgen, Kristofer M.; Hogg, Carolyn J.; Isobe, Sachiko; Jakobsen, Kjetill Sigurd; Janke, Axel; Jarvis, Erich D.; Johnson, Warren E.; Jones, Steven J.M.; Karlsson, Elinor K.; Kersey, Paul J.; Kim, Jin-Hyoung; Kress, W. John; Kuraku, Shigehiro; Lawniczak, Mara K.N.; Leebens-Mack, James H.; Li, Xueyan; Lindblad-Toh, Kerstin; Liu, Xin; Lopez, Jose V.; Marques-Bonet, Tomas; Mazard, Sophie; Mazet, Jonna A.K.; Mazzoni, Camila J.; Myers, Eugene W.; O’Neill, Rachel J.; Paez, Sadye; Park, Hyun; Robinson, Gene E.; Roquet, Cristina; Ryder, Oliver A.; Sabir, Jamal S.M.; Shaffer, H. Bradley; Shank, Timothy M.; Sherkow, Jacob S.; Soltis, Pamela S.; Tang, Boping; Tedersoo, Leho; Uliano-Silva, Marcela; Wang, Kun; Wei, Xiaofeng; Wetzer, Regina; Wilson, Julia L.; Xu, Xun; Yang, Huanming; Yoder, Anne D.; Zhang, Guojie (Peer reviewed; Journal article, 2022) -
The era of reference genomes in conservation genomics
Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; Crottini, Angelica; Godoy, José A.; Höglund, Jacob; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Svardal, Hannes; Theofanopoulou, Constantina; de Vries, Jantina; Waldvogel, Ann-Marie; Zhang, Guojie; Mazzoni, Camila J.; Jarvis, Erich D.; Bálint, Miklós; Čiampor, Fedor; Aghayan, Sargis A.; Alioto, Tyler S.; Almudí, Isabel; Alvarez, Nadir; Alves, Paulo C.; Amorim, Isabel R.; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Berg, Paul Ragnar; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, L. Filipe; Chueca, Luis J.; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V.; Delsuc, Frédéric; Dennis, Alice B.; Dimitrov, Dimitar; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Jakobsen, Kjetill Sigurd; Jentoft, Sissel; Matschiner, Michael (Peer reviewed; Journal article, 2022)Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique ... -
Evolution of the germline mutation rate across vertebrates
Bergeron, Lucie A.; Besenbacher, Søren; Zheng, Jiao; Li, Panyi; Bertelsen, Mads Frost; Quintard, Benoit; Hoffman, Joseph I.; Li, Zhipeng; St. Leger, Judy; Shao, Changwei; Stiller, Josefin; Gilbert, Marcus Thomas Pius; Schierup, Mikkel H.; Zhang, Guojie (Peer reviewed; Journal article, 2023)The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single ... -
Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet
Gelabert, Pere; Sandoval-Velasco, Marcela; Serres, Aitor; de Manuel, Marc; Renom, Pere; Margaryan, Ashot; Stiller, Josefin; De-Dios, Toni; Fang, Qi; Feng, Shaohong; Mañosa, Santi; Pacheco, George; Ferrando-Bernal, Manuel; Shi, Guolin; Hao, Fei; Chen, Xianqing; Petersen, Bent; Olsen, Remi-André; Navarro, Arcadi; Deng, Yuan; Dalén, Love; Marques-Bonet, Tomas; Zhang, Guojie; Antunes, Agostinho; Gilbert, Marcus Thomas Pius; Lalueza-Fox, Carles (Peer reviewed; Journal article, 2020)As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati ... -
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
Seki, Ryohei; Li, Caí; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, Marcus Thomas Pius; Zhou, Qi; Xu, Xing; Shiroishi, Toshihiko; Irie, Naoki; Tamura, Koji; Zhang, Guojie (Journal article; Peer reviewed, 2017)Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous ... -
Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction
Femerling, Georgette; van Oosterhout, Cock; Feng, Shaohong; Bristol, Rachel M.; Zhang, Guojie; Groombridge, Jim; Gilbert, Marcus Thomas Pius; Morales, Hernán E (Journal article; Peer reviewed, 2023)High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher ... -
Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat, Homotherium latidens
Barnett, Ross; Westbury, Michael V; Sandoval-Velasco, Marcela; Vieira, Filipe G.; Jeon, Sungwon; Zazula, Grant; Martin, Michael David; Ho, Simon Y.W.; Mather, Niklas; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; de Manuel, Marc; Zepeda-Mendoza, Marie Lisandra; Antunes, Agostinho; Carmona Baez, Aldo; De Cahsan, Binia; Larson, Greger; O'Brien, Stephen J.; Eizirik, Eduardo; Johnson, Warren E.; Koepfli, Klaus-Peter; Wilting, Andreas; Fickel, Jörns; Dalén, Love; Lorenzen, Eline D.; Marques-Bonet, Tomas; Hansen, Anders J.; Zhang, Guojie; Bhak, Jong; Yamaguchi, Nobuyuki; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2020)Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated ... -
Genomic insights into the secondary aquatic transition of penguins
Cole, Theresa L.; Zhou, Chengran; Fang, Miaoquan; Pan, Hailin; Ksepka, Daniel T.; Fiddaman, Steven R.; Emerling, Christopher A.; Thomas, Daniel B.; Bi, Xupeng; Fang, Qi; Ellegaard, Martin Rene; Feng, Shaohong; Smith, Adrian L.; Heath, Tracy A.; Tennyson, Alan J. D.; Borboroglu, Pablo García; Wood, Jamie R.; Hadden, Peter W.; Grosser, Stefanie; Bost, Charles-André; Cherel, Yves; Mattern, Thomas; Hart, Tom; Sinding, Mikkel Holger Strander; Shepherd, Lara D.; Phillips, Richard A.; Quillfeldt, Petra; Masello, Juan F.; Bouzat, Juan L.; Ryan, Peter G.; Thompson, David R.; Ellenberg, Ursula; Dann, Peter; Miller, Gary; Dee Boersma, Boersma; Zhao, Ruoping; Gilbert, Marcus Thomas Pius; Yang, Huanming; Zhang, De-Xing; Zhang, Guojie (Journal article; Peer reviewed, 2022) -
The germline mutational process in rhesus macaque and its implications for phylogenetic dating
Bergeron, Lucie A.; Besenbacher, Søren; Bakker, Jaco; Zheng, Jiao; Li, Panyi; Pacheco, George; Sinding, Mikkel-Holger S.; Kamilari, Maria; Gilbert, Marcus Thomas Pius; Schiedrup, Mikkel H.; Zhang, Guojie (Peer reviewed; Journal article, 2021)Background Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Results Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca ... -
High-coverage genomes to elucidate the evolution of penguins
Pan, Hailin; Cole, Theresa L.; Bi, Xupeng; Fang, Miaoquan; Zhou, Chengran; Yang, Zhengtao; Ksepka, Daniel T.; Hart, Tom; Bouzat, Juan L.; Argilla, Lisa S.; Bertelsen, Mads F.; Boersma, P. Dee; Bost, Charles-André; Cherel, Yves; Dann, Peter; Fiddaman, Steven R.; Howard, Pauline; Labuschagne, Kim; Mattern, Thomas; Miller, Gary; Parker, Patricia; Phillips, Richard A.; Quillfeldt, Petra; Ryan, Peter G.; Taylor, Helen; Thompson, David R.; Young, Melanie J.; Ellegaard, Martin; Gilbert, Marcus Thomas Pius; Sinding, Mikkel Holger Strander; Pacheco, George; Shepherd, Lara D.; Tennyson, Alan J.D.; Grosser, Stefanie; Kay, Emily; Nupen, Lisa J.; Ellenberg, Ursula; Houston, David M.; Reeve, Andrew Hart; Johnson, Kathryn; Masello, Juan F.; Stracke, Thomas; McKinlay, Bruce; Borboroglu, Pablo García; Zhang, De-Xing; Zhang, Guojie (Peer reviewed; Journal article, 2019)Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes ... -
Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
Sánchez-Barreiro, Fátima; De Cahsan, Binia; Westbury, Michael V.; Sun, Xin; Margaryan, Ashot; Fontsere, Claudia; Bruford, Michael W.; Russo, Isa-Rita M; Kalthoff, Daniela C.; Sicheritz-Pontén, Thomas; Petersen, Bent; Dalén, Love; Zhang, Guojie; Marquès-Bonet, Tomás; Gilbert, Marcus Thomas Pius; Moodley, Yoshan (Peer reviewed; Journal article, 2023)The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the ... -
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)
Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ... -
How genomics can help biodiversity conservation
Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R.; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; de Vries, Jan; Waldvogel, Ann-Marie; Zhang, Guojie; Jarvis, Erich D.; Bálint, Miklós; Ciofi, Claudio; Waterhouse, Robert M.; Mazzoni, Camila J.; Höglund, Jacob; Aghayan, Sargis A.; Alioto, Tyler S.; Almudí, Isabel; Alvarez, Nadir; Alves, Paulo C.; do Rosario, Isabel R. Amorim; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, L. Filipe C.; Chueca, Luis J.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Jakobsen, Kjetill Sigurd; Matschiner, Michael; Zammit, Gabrielle (Journal article; Peer reviewed, 2023)The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main ... -
Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal
Feuerborn, Tatiana R.; Carmagnini, Alberto; Losey, Robert J.; Nomokonova, Tatiana; Askeyev, Arthur; Askeyev, Igor; Askeyev, Oleg; Antipina, Ekaterina E.; Appelt, Martin; Bachura, Olga P.; Beglane, Fiona; Bradley, Daniel G.; Daly, Kevin G.; Gopalakrishnan, Shyam; Gregersen, Kristian Murphy; Guo, Chunxue; Gusev, Andrei V.; Jones, Carleton; Kosintsev, Pavel A.; Kuzmin, Yaroslav V.; Mattiangeli, Valeria; Perri, Angela R.; Plekhanov, Andrei; Ramos-Madrigal, Jazmín; Schmidt, Anne Lisbeth; Shaymuratova, Dilyara; Smith, Oliver; Yavorskaya, Lilia V.; Zhang, Guojie; Willerslev, Eske; Meldgaard, Morten; Gilbert, Marcus Thomas Pius; Larson, Greger; Dalén, Love; Hansen, Anders J.; Sinding, Mikkel-Holger S.; Frantz, Laurent (Peer reviewed; Journal article, 2021)Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited ... -
Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus
Fotakis, Anna K.; Denham, Sean Dexter; Mackie, Meaghan; Orbegozo, Miren Iraeta; Mylopotamitaki, Dorothea; Gopalakrishnan, Shyam; Sicheritz-Pontén, Thomas; Olsen, Jesper V.; Cappellini, Enrico; Zhang, Guojie; Christophersen, Axel; Gilbert, Thomas; Vågene, Åshild J (Peer reviewed; Journal article, 2020)Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing ...